General Biology: Atomic Structure, Chemical Bonds, and Biological Macromolecules

Atomic Structure and Subatomic Particles

Atoms and Their Components

Atoms are the fundamental units of matter, composed of subatomic particles that determine their properties and behavior in chemical reactions.

• Protons: Positively charged particles located in the nucleus. The number of protons defines the atomic number of an element.

• Neutrons: Neutral particles also found in the nucleus. The sum of protons and neutrons gives the mass number.

• Electrons: Negatively charged particles that orbit the nucleus in electron shells.

Example: Iron (Fe) has an atomic number of 26 and a mass number of 56. Therefore, it contains 26 protons, 26 electrons (in a neutral atom), and 30 neutrons (56 - 26 = 30).

Chemical Bonds and Interactions

Types of Chemical Bonds

Chemical bonds are forces that hold atoms together in molecules and compounds. The main types include:

• Covalent Bonds: Atoms share pairs of electrons. Can be nonpolar (equal sharing) or polar (unequal sharing).

• Ionic Bonds: Electrons are transferred from one atom to another, resulting in oppositely charged ions that attract each other.

• Hydrogen Bonds: Weak attractions between a hydrogen atom covalently bonded to an electronegative atom (like O or N) and another electronegative atom.

• Van der Waals Interactions: Weak, transient attractions between molecules due to temporary dipoles.

Example: The interaction shown in the diagram (Q4) is a covalent bond, where two atoms share electrons.

Ions and Ionic Charges

When atoms gain or lose electrons, they become ions:

• Cation: Positively charged ion (loss of electrons).

• Anion: Negatively charged ion (gain of electrons).

Example: In the diagram (Q5), atom A loses an electron (becomes a cation, +1), and atom B gains an electron (becomes an anion, -1).

Functional Groups in Organic Molecules

Key Chemical Groups

Functional groups are specific groups of atoms within molecules that have characteristic properties and chemical reactivity.

• Carboxyl Group (-COOH): Acts as an acid; found in amino acids and fatty acids. Example: Circled in Q2.

• Methyl Group (-CH3): Nonpolar; affects gene expression and molecular shape. Example: Circled in Q3.

Hydrophobic and Hydrophilic Molecules

Water Interactions

Molecules can be classified based on their affinity for water:

• Hydrophilic: Water-loving; dissolve easily in water (e.g., sugars, salts).

• Hydrophobic: Water-fearing; do not dissolve in water (e.g., fats, oils).

Macromolecules: Structure and Function

Overview of Biological Macromolecules

Living organisms are composed of four major classes of macromolecules: carbohydrates, lipids, proteins, and nucleic acids. These are polymers built from monomer subunits.

Carbohydrates

Carbohydrates are sugars and their polymers, serving as energy sources and structural materials.

• Monosaccharides: Simple sugars (e.g., glucose, fructose).

• Disaccharides: Two monosaccharides joined by a glycosidic bond (e.g., sucrose).

• Polysaccharides: Long chains of monosaccharides (e.g., starch in plants, glycogen in animals, cellulose in plants, chitin in animals).

Bond Type: Glycosidic linkage.

Example: Starch is a storage polysaccharide in plants.

Lipids

Lipids are diverse hydrophobic molecules, including fats, phospholipids, and steroids.

• Fats (Triglycerides): Composed of glycerol and three fatty acids. Can be saturated (no double bonds, solid at room temperature) or unsaturated (one or more double bonds, liquid at room temperature).

• Phospholipids: Major component of cell membranes; have hydrophilic heads and hydrophobic tails.

• Steroids: Four fused carbon rings; includes cholesterol (membrane component) and hormones (e.g., testosterone, estradiol).

Example: Unsaturated fatty acids have one or more double bonds, causing kinks in the hydrocarbon chain.

Nucleic Acids

Nucleic acids store and transmit genetic information. The two main types are DNA and RNA.

• DNA (Deoxyribonucleic Acid): Double-stranded, stores genetic information.

• RNA (Ribonucleic Acid): Single-stranded, involved in gene expression and protein synthesis.

Monomer: Nucleotide, consisting of a phosphate group, a five-carbon sugar (deoxyribose in DNA, ribose in RNA), and a nitrogenous base.

Nitrogenous Bases:

• Pyrimidines: Cytosine (C), Thymine (T, in DNA), Uracil (U, in RNA)

• Purines: Adenine (A), Guanine (G)

Bond Type: Phosphodiester linkage (between nucleotides).

Example: DNA is a double helix with complementary base pairing (A-T, G-C).

Proteins

Proteins are polymers of amino acids that perform a vast array of functions in living organisms.

• Monomer: Amino acid (20 different types, each with a unique R group).

• Bond Type: Peptide bond (formed by dehydration synthesis).

• Functions: Enzymatic catalysis, defense (antibodies), transport (hemoglobin), storage, signaling (hormones), movement (muscle proteins), structural support (collagen, keratin).

Levels of Protein Structure:

• Primary: Sequence of amino acids.

• Secondary: Local folding (α-helix, β-pleated sheet) due to hydrogen bonding.

• Tertiary: Overall 3D shape from interactions among side chains (hydrogen bonds, ionic bonds, hydrophobic interactions, disulfide bridges).

• Quaternary: Association of multiple polypeptide chains (not all proteins have this level).

Example: Hemoglobin is a quaternary protein composed of four polypeptide subunits.

Summary Table: Macromolecules

Molecule	Monomer	Polymer	Bond Name	Function
Carbohydrates	Monosaccharide	Polysaccharide	Glycosidic linkage	Energy storage, structure
Lipids	Glycerol, fatty acids	Triglyceride, phospholipid, steroid	Ester bond	Energy storage, membranes, signaling
Nucleic Acids	Nucleotide	Polynucleotide (DNA/RNA)	Phosphodiester linkage	Genetic information storage and transfer
Proteins	Amino acid	Polypeptide	Peptide bond	Catalysis, structure, transport, defense, signaling

Study and Exam Preparation Tips

• Review lecture slides and reorganize notes for clarity.

• Rewrite confusing topics in your own words.

• Use online study tools and practice quizzes.

• Identify and seek help for challenging concepts.

• Plan a specific study schedule and take breaks.

Key Equations and Concepts

• Number of Neutrons: $\text{Number of neutrons} = \text{Mass number} - \text{Atomic number}$

• Molarity: $\text{Molarity} = \frac{\text{moles of solute}}{\text{liters of solution}}$

Additional info: Some diagrams and chemical structures were interpreted based on standard biology curriculum. The summary table was expanded for clarity and completeness.